We have clients who are required to have both Type I and Type II NPI Numbers - even though they are sole proprietors - because they are doing business as a legal entity with an Employer ID Number (as opposed to a Taxpayer ID Number). Payment is made to the Employer ID Number - hence the required designation for who gets paid (the Type II NPI #). At least for Medicare, they also want the NPI # for who did the work. Hence, the Type I NPI #.
Remember that an organization can get paid (Type II), but it can never do the work. The work must always be done by a real person (Type I), who can also be the entity which gets paid (either by Taxpayer ID # = Type I, or Employer ID # = Type II).
Jessica - in your case, it appears that your providers are employees, paid by your non-profit organization. In your case, the non-profit is the billing entity - so bills should be submitted with their Type II NPI # on it (who gets paid). Medicare at least will require the Type 1 NPI # on the CMS 1500 also (who did the work). That number will be assigned to the individual doctors employed by your non-profit. The Type I NPI # of the doctor for whose work you are billing needs to be included on any CMS 1500 Form submitted to Medicare (and others who might require it). That number will vary, depending on which doctor's work you are billing for. But the Type II NPI # of the billing entity, your non-profit, the who gets paid, will stay the same on all billing for a given discipline.